I know nothing about Atmel Studio 7, but beware that Windows "partitions" an SDcard differently than Linux.
That is, Windows does not install a (MBR) partition table on SDcards, whereas Linux installs a MBR and partition table in the first sector.
IOW WIndows treats the SDcard like a floppy diskette, whereas Linux treats it like a HDD.

However your SDcard is formatted, try redoing it using the other OS.
But first obliterate the existing partitioning using the Linux shell command `dd if=/dev/null of=/dev/sdX count=63` for best results (replace X with the proper device letter, which is probably something other than `a`).